Water that's leaking into your commercial building is bad news and needs to be addressed immediately. Your first reaction might be to contact a roofing contractor to come out and repair the roof. However, many times, the water entry stems not by a roof failure, but via HVAC side discharge duct work that has lost its integrity. Check out these videos, taken during HVAC duct work inspections.
The water in the duct work shown here is the result of tests conducted after the building owners discovered water draining into the building through the HVAC system. In both cases, water penetration had nothing to do with the roofing system.
In our experience, it's not a question of "if" the side discharge duct will leak, it's "when." Metal joints that are exposed to the elements are held together by screws, rivets or caulk that age and lose their integrity over time because of metal expansion and contraction. Water then enters the HVAC system due to suction created by air flow, blowing rain, and/or rust.
Ideally, at the start of the construction project, building owners should invest in curbs that HVAC units "sit" on, and direct air through, straight down into the building; no side discharge ducting is involved. (See the image below.)
Of course, if the side discharge duct work is already in place, you should inspect it frequently to ensure it maintains its integrity. At the earliest sign that it may not be watertight, you should call a qualified and reputable HVAC maintenance professional to make necessary repairs.